JAL-3010 offer 'apply to all {parent SO term} features' where applicable

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cd7d1af..9356ad1 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -326,7 +326,7 @@ public class Jalview
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault("USE_FULL_SO", false))
+    if (Cache.getDefault("USE_FULL_SO", true))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
@@ -538,7 +538,8 @@ public class Jalview
           data.replaceAll("%20", " ");
 
           ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport().getAlignment(), data);
+                  .getColourScheme(af.getViewport(),
+                          af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
@@ -828,9 +829,6 @@ public class Jalview
                     // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
-                    + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
-                    + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
-                    + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     // +
                     // "-vdoc vamsas-document\tImport vamsas document into new